qPCR-based mitochondrial DNA quantification: Influence of template DNA fragmentation on accuracy

Real-time PCR (qPCR) is the method of choice for quantification of mitochondrial DNA (mtDNA) by relative comparison of a nuclear to a mitochondrial locus. Quantitative abnormal mtDNA content is indicative of mitochondrial disorders and mostly confines in a tissue-specific manner. Thus handling of degradation-prone bioptic material is inevitable. We established a serial qPCR assay based on increasing amplicon size to measure degradation status of any DNA sample. Using this approach we can exclude erroneous mtDNA quantification due to degraded samples (e.g. long post-exicision time, autolytic processus, freeze-thaw cycles) and ensure abnormal DNA content measurements (e.g. depletion) in non-degraded patient material. By preparation of degraded DNA under controlled conditions using sonification and DNaseI digestion we show that erroneous quantification is due to the different preservation qualities of the nuclear and the mitochondrial genome. This disparate degradation of the two genomes results in over- or underestimation of mtDNA copy number in degraded samples. Moreover, as analysis of defined archival tissue would allow to precise the molecular pathomechanism of mitochondrial disorders presenting with abnormal mtDNA content, we compared fresh frozen (FF) with formalin-fixed paraffin-embedded (FFPE) skeletal muscle tissue of the same sample. By extrapolation of measured decay constants for nuclear DNA (λnDNA) and mtDNA (λmtDNA) we present an approach to possibly correct measurements in degraded samples in the future. To our knowledge this is the first time different degradation impact of the two genomes is demonstrated and which evaluates systematically the impact of DNA degradation on quantification of mtDNA copy number.

Intraoperative template-molded bone flap reconstruction for patient-specific cranioplasty

Cranioplasty is a common neurosurgical procedure. Free-hand molding of polymethyl methacrylate (PMMA) cement into complex three-dimensional shapes is often time-consuming and may result in disappointing cosmetic outcomes. Computer-assisted patient-specific implants address these disadvantages but are associated with long production times and high costs. In this study, we evaluated the clinical, radiological, and cosmetic outcomes of a time-saving and inexpensive intraoperative method to mold custom-made implants for immediate single-stage or delayed cranioplasty. Data were collected from patients in whom cranioplasty became necessary after removal of bone flaps affected by intracranial infection, tumor invasion, or trauma. A PMMA replica was cast between a negative form of the patient's own bone flap and the original bone flap with exactly the same shape, thickness, and dimensions. Clinical and radiological follow-up was performed 2 months post-surgery. Patient satisfaction (Odom criteria) and cosmesis (visual analogue scale for cosmesis) were evaluated 1 to 3 years after cranioplasty. Twenty-seven patients underwent intraoperative template-molded patient-specific cranioplasty with PMMA. The indications for cranioplasty included bone flap infection (56%, n = 15), calvarian tumor resection (37%, n = 10), and defect after trauma (7%, n = 2). The mean duration of the molding procedure was 19 ± 7 min. Excellent radiological implant alignment was achieved in 94% of the cases. All (n = 23) but one patient rated the cosmetic outcome (mean 1.4 years after cranioplasty) as excellent (70%, n = 16) or good (26%, n = 6). Intraoperative cast-molded reconstructive cranioplasty is a feasible, accurate, fast, and cost-efficient technique that results in excellent cosmetic outcomes, even with large and complex skull defects.

Open top chambers and infrared lamps : a comparison of heating efficacy and CO₂/CH₄ dynamics in a Lake Superior coastal peatland

Experimental warming provides a method to determine how an ecosystem will respond to increased temperatures. Northern peatland ecosystems, sensitive to changing climates, provide an excellent setting for experimental warming. Storing great quantities of carbon, northern peatlands play a critical role in regulating global temperatures. Two of the most common methods of experimental warming include open top chambers (OTCs) and infrared (IR) lamps. These warming systems have been used in many ecosystems throughout the world, yet their efficacy to create a warmer environment is variable and has not been widely studied. To date, there has not been a direct, experimentally controlled comparison of OTCs and IR lamps. As a result, a factorial study was implemented to compare the warming efficacy of OTCs and IR lamps and to examine the resulting carbon dioxide (CO2) and methane (CH4) flux rates in a Lake Superior peatland. IR lamps warmed the ecosystem on average by 1-2 #°C, with the majority of warming occurring during nighttime hours. OTC's did not provide any long-term warming above control plots, which is contrary to similar OTC studies at high latitudes. By investigating diurnal heating patterns and micrometeorological variables, we were able to conclude that OTCs were not achieving strong daytime heating peaks and were often cooler than control plots during nighttime hours. Temperate day-length, cloudy and humid conditions, and latent heat loss were factors that inhibited OTC warming. There were no changes in CO2 flux between warming treatments in lawn plots. Gross ecosystem production was significantly greater in IR lamp-hummock plots, while ecosystem respiration was not affected. CH4 flux was not significantly affected by warming treatment. Minimal daytime heating differences, high ambient temperatures, decay resistant substrate, as well as other factors suppressed significant gas flux responses from warming treatments.

A systematic review on the accuracy and the clinical outcome of computer-guided template-based implant dentistry

Introduction: The aim of this systematic review was to analyze the dental literature regarding accuracy and clinical application in computer-guided template-based implant dentistry. Materials and methods: An electronic literature search complemented by manual searching was performed to gather data on accuracy and surgical, biological and prosthetic complications in connection with computer-guided implant treatment. For the assessment of accuracy meta-regression analysis was performed. Complication rates are descriptively summarized. Results: From 3120 titles after the literature search, eight articles met the inclusion criteria regarding accuracy and 10 regarding the clinical performance. Meta-regression analysis revealed a mean deviation at the entry point of 1.07 mm (95% CI: 0.76-1.22 mm) and at the apex of 1.63 mm (95% CI: 1.26-2 mm). No significant differences between the studies were found regarding method of template production or template support and stabilization. Early surgical complications occurred in 9.1%, early prosthetic complications in 18.8% and late prosthetic complications in 12% of the cases. Implant survival rates of 91-100% after an observation time of 12-60 months are reported in six clinical studies with 537 implants mainly restored immediately after flapless implantation procedures. Conclusion: Computer-guided template-based implant placement showed high implant survival rates ranging from 91% to 100%. However, a considerable number of technique-related perioperative complications were observed. Preclinical and clinical studies indicated a reasonable mean accuracy with relatively high maximum deviations. Future research should be directed to increase the number of clinical studies with longer observation periods and to improve the systems in terms of perioperative handling, accuracy and prosthetic complications.

A three-dimensional histological atlas of the human basal ganglia. II. Atlas deformation strategy and evaluation in deep brain stimulation for Parkinson disease

OBJECT: The localization of any given target in the brain has become a challenging issue because of the increased use of deep brain stimulation to treat Parkinson disease, dystonia, and nonmotor diseases (for example, Tourette syndrome, obsessive compulsive disorders, and depression). The aim of this study was to develop an automated method of adapting an atlas of the human basal ganglia to the brains of individual patients. METHODS: Magnetic resonance images of the brain specimen were obtained before extraction from the skull and histological processing. Adaptation of the atlas to individual patient anatomy was performed by reshaping the atlas MR images to the images obtained in the individual patient using a hierarchical registration applied to a region of interest centered on the basal ganglia, and then applying the reshaping matrix to the atlas surfaces. RESULTS: Results were evaluated by direct visual inspection of the structures visible on MR images and atlas anatomy, by comparison with electrophysiological intraoperative data, and with previous atlas studies in patients with Parkinson disease. The method was both robust and accurate, never failing to provide an anatomically reliable atlas to patient registration. The registration obtained did not exceed a 1-mm mismatch with the electrophysiological signatures in the region of the subthalamic nucleus. CONCLUSIONS: This registration method applied to the basal ganglia atlas forms a powerful and reliable method for determining deep brain stimulation targets within the basal ganglia of individual patients.

Mineralization of calcium phosphate crystals in starch template inducing a brushite kidney stone biomimetic composite

Dicalcium phosphate dihydrate (brushite) and octacalcium phosphate (OCP) crystals are precursors of hydroxyapatite (HAp) for tooth enamel, dentine, and bones formation in living organisms. Here, we introduce a new method for biomimicking brushite and OCP in starch using single and double diffusion techniques. Brushite and OCP crystals were grown by precipitation in starch after gelation. The obtained materials were analyzed by infrared spectroscopy (IR), scanning electron microscopy (SEM), X-ray diffraction (XRD), and confocal laser scanning microscopy (CLSM). IR spectra demonstrate starch inclusion by peak shifts in the 2900–3500 cm–1 region. SEM showed two different morphologies: plate-shaped and needle-like crystals. Calcium phosphate/starch aggregates bear strong resemblance to prismatic brushite kidney stones. This may open up a clue to understand the mechanism of kidney stone formation.

Search for charged Higgs bosons through the violation of lepton universality in t art events using collision data at sqrts=7 TeV with the AT experiment

In several extensions of the Standard Model, the top quark can decay into a bottom quark and a light charged Higgs boson H+, t -> bH(+), in addition to the Standard Model decay t -> bW. Since W bosons decay to the three lepton generations equally, while H+ may predominantly decay into tau nu, charged Higgs bosons can be searched for using the violation of lepton universality in top quark decays. The analysis in this paper is based on 4.6 fb(-1) of proton-proton collision data at root s = 7 TeV collected by the ATLAS experiment at the Large Hadron Collider. Signatures containing leptons (e or mu) and/or a hadronically decaying tau (tau(had)) are used. Event yield ratios between e+ tau(had) and e + mu, as well as between mu + tau(had) and mu + e, final states are measured in the data and compared to predictions from simulations. This ratio-based method reduces the impact of systematic uncertainties in the analysis. No significant deviation from the Standard Model predictions is observed. With the assumption that the branching fraction B(H+ -> tau nu) is 100%, upper limits in the range 3.2%-4.4% can be placed on the branching fraction B(t -> bH(+)) for charged Higgs boson masses m(H+) in the range 90-140GeV. After combination with results from a search for charged Higgs bosons in t (t) over bar decays using the tau(had) + jets final state, upper limits on B(t -> bH(+)) can be set in the range 0.8%-3.4%, for m(H+) in the range 90-160GeV.

Measurement of the ttbar production cross section in the tau+jets channel using the ATLAS detector

A measurement of the top quark pair production cross section in the final state with a hadronically decaying tau lepton and jets is presented. The analysis is based on proton-proton collision data recorded by the ATLAS experiment at the LHC, with a centre-of-mass energy of 7 TeV. The data sample corresponds to an integrated luminosity of 1.67 fb(-1). The cross section is measured to be sigma(t (t) over bar) = 194 +/- 18 (stat.) +/- 46 (syst.) pb and is in agreement with other measurements and with the Standard Model prediction.

Performance of jet substructure techniques for large-ℝ jets in proton-proton collisions at sqrts = 7 TeV using the ATLAS detector

This paper presents the application of a variety of techniques to study jet substructure. The performance of various modified jet algorithms, or jet grooming techniques, for several jet types and event topologies is investigated for jets with transverse momentum larger than 300 GeV. Properties of jets subjected to the mass-drop filtering, trimming, and pruning algorithms are found to have reduced sensitivity to multiple proton-proton interactions, are more stable at high luminosity and improve the physics potential of searches for heavy boosted objects. Studies of the expected discrimination power of jet mass and jet substructure observables in searches for new physics are also presented. Event samples enriched in boosted W and Z bosons and top-quark pairs are used to study both the individual jet invariant mass scales and the efficacy of algorithms to tag boosted hadronic objects. The analyses presented use the full 2011 ATLAS dataset, corresponding to an integrated luminosity of 4.7 +/- 0.1 /fb from proton-proton collisions produced by the Large Hadron Collider at a center-of-mass energy of sqrt(s) = 7 TeV.

Search for direct third-generation squark pair production in final states with missing transverse momentum and two b-jets in sqrts = 8 TeV pp collisions with the ATLAS detector

The results of a search for pair production of supersymmetric partners of the Standard Model third-generation quarks are reported. This search uses 20.1 fb(-1) of pp collisions at root s = 8 TeV collected by the ATLAS experiment at the Large Hadron Collider. The lightest bottom and top squarks ((b) over tilde (1) and (t) over tilde (1) respectively) are searched for in a final state with large missing transverse momentum and two jets identified as originating from b-quarks. No excess of events above the expected level of Standard Model background is found. The results are used to set upper limits on the visible cross section for processes beyond the Standard Model. Exclusion limits at the 95% confidence level on the masses of the third-generation squarks are derived in phenomenological supersymmetric R-parity-conserving models in which either the bottom or the top squark is the lightest squark. The (b) over tilde (1) is assumed to decay via (b) over tilde (1) -> b (chi) over tilde (0)(1) and the (t) over tilde (1) via (t) over tilde (1) b (chi) over tilde (+/-)(1), with undetectable products of the subsequent decay of the (chi) over tilde (+/-)(1) due to the small mass splitting between the (chi) over tilde (+/-)(1) and the (chi) over tilde (0)(1)

A search for ttbar resonances in the lepton plus jets final state with ATLAS using 4.7 fb⁻¹ of collisions at sqrt(s) = 7 TeV

A search for new particles that decay into top quark pairs (t (t) over bar) is performed with the ATLAS experiment at the LHC using an integrated luminosity of 4.7 fb(-1) of proton-proton (pp) collision data collected at a center-of-mass energy root s = 7 TeV. In the t (t) over bar) -> WbWb decay, the lepton plus jets final state is used, where one W boson decays leptonically and the other hadronically. The t (t) over bar) system is reconstructed using both small-radius and large-radius jets, the latter being supplemented by a jet substructure analysis. A search for local excesses in the number of data events compared to the Standard Model expectation in the t (t) over bar) invariant mass spectrum is performed. No evidence for a t (t) over bar) resonance is found and 95% credibility-level limits on the production rate are determined for massive states predicted in two benchmark models. The upper limits on the cross section times branching ratio of a narrow Z' resonance range from 5.1 pb for a boson mass of 0.5 TeV to 0.03 pb for a mass of 3 TeV. A narrow leptophobic topcolor Z' resonance with a mass below 1.74 TeV is excluded. Limits are also derived for a broad color-octet resonance with m 15.3%. A Kaluza-Klein excitation of the gluon in a Randall-Sundrum model is excluded for masses below 2.07 TeV.

Measurement with the ATLAS detector of multi-particle azimuthal correlations in p+Pb collisions at sqrtsNN=5.02 TeV

In order to study further the long-range correlations ("ridge") observed recently in p+Pb collisions at sqrt(s_NN) =5.02 TeV, the second-order azimuthal anisotropy parameter of charged particles, v_2, has been measured with the cumulant method using the ATLAS detector at the LHC. In a data sample corresponding to an integrated luminosity of approximately 1 microb^(-1), the parameter v_2 has been obtained using two- and four-particle cumulants over the pseudorapidity range |eta|<2.5. The results are presented as a function of transverse momentum and the event activity, defined in terms of the transverse energy summed over 3.1methods, and to predictions from hydrodynamic models of p+Pb collisions. Despite the small transverse spatial extent of the p+Pb collision system, the large magnitude of v_2 and its similarity to hydrodynamic predictions provide additional evidence for the importance of final-state effects in p+Pb reactions.

Search for a light charged Higgs boson in the decay channel H⁺ o c ars in t art events using collisions at sqrts = 7 TeV with the ATLAS detector

A search for a charged Higgs boson (H+) in t (t) over bar decays is presented, where one of the top quarks decays via t -> H(+)b, followed by H+ -> two jets (c (s) over bar). The other top quark decays to Wb, where the W boson then decays into a lepton (e/mu) and a neutrino. The data were recorded in pp collisions at root s = 7 TeV by the ATLAS detector at the LHC in 2011, and correspond to an integrated luminosity of 4.7 fb(-1). With no observation of a signal, 95 % confidence level (CL) upper limits are set on the decay branching ratio of top quarks to charged Higgs bosons varying between 5 % and 1 % for H+ masses between 90 GeV and 150 GeV, assuming B(H+ -> c (s) over bar) = 100 %.

Measurement of kT splitting scales in W→lv events at sqrt(s)=7 TeV with the ATLAS detector

A measurement of splitting scales, as defined by the kT clustering algorithm, is presented for final states containing a W boson produced in proton-proton collisions at a centre-of-mass energy of 7 TeV. The measurement is based on the full 2010 data sample corresponding to an integrated luminosity of 36 pb(-1) which was collected using the ATLAS detector at the CERN Large Hadron Collider. Cluster splitting scales are measured in events containing W bosons decaying to electrons or muons. The measurement comprises the four hardest splitting scales in a k(T) cluster sequence of the hadronic activity accompanying the W boson, and ratios of these splitting scales. Backgrounds such as multi-jet and top-quark-pair production are subtracted and the results are corrected for detector effects. Predictions from various Monte Carlo event generators at particle level are compared to the data. Overall, reasonable agreement is found with all generators, but larger deviations between the predictions and the data are evident in the soft regions of the splitting scales.

Search for single b*-quark production with the ATLAS detector at sqrts=7 TeV

The results of a search for an excited bottom-quark b* in pp collisions at root s = 7 TeV, using 4.7 fb(-1) of data collected by the ATLAS detector at the LHC are presented. In the model studied, a single b*-quark is produced through a chromomagnetic interaction and subsequently decays to a W boson and a top quark. The search is performed in the dilepton and lepton + jets final states, which are combined to set limits on b*-quark couplings for a range of b*-quark masses. For a benchmark with unit size chromomagnetic and Standard Model-like electroweak b* couplings, b* quarks with masses less than 870 GeV are excluded at the 95% credibility level.